I've never understood this complaint about Lincoln and the Civil War. There are only two ways to look at it:
1) The union was intended to be perpetual and secession illegal, and so saying they are seceding is to engage in rebellion and become reasonable targets for law enforcement and to have the rebellion quashed, particularly once military action was taken against Ft. Sumter and a number of other federal forts.
2) The notion that any union or confederation is perpetual is pretty lame. We acknowledge the reality of the situation, several states seceded from the union and formed their own confederation of states, their own country with its own capital. At this point it was entirely within the rights of the US to engage in open war with the new country, retake their lands, and incorporate it back into the US, again especially after federal lands and facilities were attacked.
Lincoln was of the first school of thought. President Buchanan before him was also of the first school of thought, but he didn't believe it was within the rights of the constitution to attack a state in open rebellion against the country, which seems like a bit of a logical dilemma. Of course, he didn't have to really deal with the secession problem for more than a couple months, so I guess we can forgive him for not having a logically consistent framework for how to deal with things.
Personally, I subscribe to the second school of thought. I think it is more realistic and accepting of practical truths.
Also, while you are right that the Civil War was not fought over any proactive interest in radical emancipation of slaves, it was indeed fought about slavery as a practice and what its future in the US would be. Lincoln was against slavery on a moral basis and prior to his election spoke in support of it being abolished over time, but he was not in favor of forcibly (through law or otherwise) ending slavery in the southern slave states on any immediate timetable. The problem was predominantly about southern state's fears about slavery slowly "going out of style" by virtue of the pattern of western territories and the non-slave states not being willing to grant or enforce slave property laws. The new territories were predominantly being founded as non-slave states, much to the dismay of the slave states. They saw the practice of slavery crumbling in the long run if it was not expanded into use in the new states. And despite all the "states rights" rhetoric used to wrap the slave ownership issue, the slave states were very much in favor of federal laws and enforcement in all the states of various slave property rights. Slave owners who traveled with their slaves into non-slave states wanted their slave ownership rights protected despite the laws against slavery in those states, they wanted escaped slaves in non-slave states to be considered slaves still and thus returned to their owners, and various other measures.
The south saw the end to slavery coming, inexorably, at some point in the future and in the near term they saw their property interests in slaves being ignored by the other states and in federal law enforcement and their power to project slavery into the new territories limited. So they seceded, trying to head off fate and determine their own slave owning destinies without Republican/Northern interruption.
As for the post-war claims of it being about states rights, not specifically slavery... Much of this is given legs to stand on only by the passage of a number of laws during the war, which were not about slavery and had been being blocked by the southern state delegations for some time prior to their secession. Some laws were passed due to the war which were also against a state's rights perspective, such as the imposition of a federal income tax to pay for the war. To claim the principle reason for the war was these other laws and issues besides slavery, however, is revisionism, plain and simple.
The south was fighting a losing battle, in every sense, when it came to slavery. Perhaps the Civil War could have been avoided, but given the base issues at play with regard to slavery and the rather inciting act of mass secession... it was going to happen, either according to the first or second school of thought.